Suppressing Doxygen warnings

You could use suppression tags in the generated files:

//! @cond Doxygen_Suppress
code
//! @endcond

You don't need the "Doxygen_Suppress" in there, but I like it for clarity.

There are more options in the doxygen FAQ

EDIT: Ok, I should have done my due diligence, I have an answer that is more appropriate to your situation. I believe you need to exclude the files entirely. Add this to your doxygen file:

# The EXCLUDE tag can be used to specify files and/or directories that should 
# excluded from the INPUT source files. This way you can easily exclude a 
# subdirectory from a directory tree whose root is specified with the INPUT tag.

EXCLUDE                = abc.cpp \
                         abc.h

The irony is I have had this problem and solved it, then forgot all about it... Brain must be full again.

I pulled this information from the doxygen Configuration page, but if you are lazy like me, just use the gui tool (doxywizard) and go through and select all the things you want and have it save the doxyfile for you.

There's a config option for that, as stated in documentation

WARN_IF_UNDOCUMENTED

If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag will automatically be disabled.